I'm not sure if the VS55 can handle KT88's. A lot of ARC's can even though they don't support it. And, KT88's will definitely sound different (and different brands of KT88's sound different from each other as well) so it pays to think about what sound you are trying to make before you leap.
One of the principal reasons ARC wants folks to use SED6550's (OEM tube) is that they are rugged and rarely fail. (Many popular KT88's are not rugged, i.e. they are failure prone) This has been important because their biasing circuit is not fused and if a power tube shorts out it will take out a resistor in the bias circuit as well as the main fuse. The latter's no big deal, but unless you are handy you have to find a techie to install a new resistor. I had to send my amp back to ARC for repairs, a PITA.
Again, Im not familar with your amp. But I'd be inclined to follow thier advise. Besides, I like SED 6550's in several non-ARC amps I use as well as the ARC I used to use.